A committee of MPs has called for a cabinet minister and senior civil servants to resign or be sacked after the failure of the Rural Payments Agency's (RPA) IT project to implement the Single Payments Scheme (SPS) for farmers.

In a scathing report, the Commons environment, food and rural affairs committee said former environment secretary Margaret Beckett – now foreign secretary – and Sir Brian Bender, the former permanent secretary at the Department of Environment, Food and Rural Affairs (Defra), should be held accountable for the failure.

The huge IT project to implement the SPS – which consolidates 11 separate European Union subsidies – descended into chaos, leaving farmers out of pocket by a total of up to £22.5 million (US$44 million). The cost to Defra runs into hundreds of millions of pounds, while only £7.5 million of £164 million planned savings has materialised.

Committee chair Michael Jack MP said: "The report confirms that responsibility and accountability stretches from the top of Defra all the way to the Rural Payments Agency, but so far only one man has paid for this failure by losing his job: the former RPA chief executive Johnston McNeill.

"We believe if accountability is to mean anything then the position of others must now be seriously questioned. Those involved should examine their consciences about the role they played in this failed venture, which could well cost Defra and farmers up to half a billion pounds."

The report says Defra's failure to carry out one of its core functions in line with its own policies is the factor that "differentiates this issue from the myriad of botched government IT projects".

It notes that the RPA took responsibility for IT design "but was not well served by its principal IT contractor," Accenture.

It said: "Accenture made an unsatisfactory start; while the RPA and Defra disagree with Accenture about whether it was late in supplying parts of the IT system, the systems it delivered were slow and unreliable and not always able to cope with the volumes of work encountered; and its systems were not user-friendly."

It cites evidence given to the MPs by McNeill, who said: "The difficulty was not that the system did not work, the difficulty was its availability to our staff and fact that the system kept falling over."

But the MPs reserved their harshest words for Beckett and her senior civil servants, arguing that they should pay the price for the RPA "catastrophe".

In a damning passage, the report says those in the Defra and RPA leadership most closely involved – Beckett, Bender and Andy Lebrecht, the director general for sustainable farming, food and fisheries – have "moved on unscathed or stayed in post", adding: "A culture where ministers and senior officials can preside over failure of this magnitude and not be held personally accountable creates a serious risk of further failures in public service delivery."

Since the debacle, Bender has become permanent secretary at the Department of Trade and Industry, while Beckett was promoted in a cabinet reshuffle to the post of foreign secretary.

Failure in a fundamental responsibility should mean the secretary of state "should not be rewarded with promotion but its reverse", the report says.

The report also calls on Defra and the RPA to cost and publish details of the further IT changes needed to overcome current problems and speed up SPS payments.